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May 15, 2019

The Insight Show Notes — Season 2, Episode 27: Neolithic Massacre

Filed under: Archaeology,History,science — Razib Khan @ 2:56 pm

The Insight Show Notes — Season 2, Episode 27: Neolithic Massacre

This week on The Insight (Apple Podcasts, Spotify, Stitcher and Google Podcasts) Razib talks to an archaeologist and geneticist who were authors of a paper that documented a Neolithic massacre of a group of people in Poland ~4,500 years ago.

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The work here is very interdisciplinary. A generation ago this would be mostly placed in the archaeological context of the culture that these individuals came from, Globular Amphora people. These are the last of the Neolithic farming societies of Northern Europe. That is the societies that derive from the expansion of agriculturalists from the southeast, originally from Anatolia (whose closest modern relatives are Sardinian).

These were replaced and assimilated about ~4,500 years ago by the steppe people, the Corded Ware culture. This site in southern Poland was situated on the border between Globular Amphora and steppe societies during a time of transitions.

The most novel aspect of this publication is that they’ve obtained whole-genome sequences, which allowed them to reconstruct patterns of kinships. Conventional archaeology of this sort focuses on age and sex, as well as the position of people buried. This paper overlaid upon that information about kinship relationships.

It was like taking a two-dimensional picture, and adding the depth of human relationships atop that, and so bringing it into a whole new area of narrative inference. Likely this is the future for these sorts of reconstructions. Prehistory will remain before history, but the genealogies of the past will come to life.


The Insight Show Notes — Season 2, Episode 27: Neolithic Massacre was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Anatomy of a prehistoric atrocity

Filed under: Archaeology,History,War — Razib Khan @ 2:12 am
A Neolithic grave pit in France

We don’t necessarily see the world of Europe before written history as uniform darkness, despite the lack of texts. Rather, we see some elements of prehistory with crystal clarity, while others remain entirely opaque to us. Prehistory does not speak in names. It is not a world of the word. But it is a world of material, from the tools of the Paleolithic to the more diverse and complex assemblances of the people of the Holocene, after the Ice Age.

What we call civilization emerged organically, but foggily, out of earlier societies which were complex, but pre-literate. The first agriculturalists of Europe and Asia did not leave histories behind, but rather artifacts and remains. Much of what we know about these people is traced by shards of pottery.

Prehistoric archaeology after the Ice Age, but before the rise of written societies, is often a matter of interpretation and cataloging of these copious material remains. Unlike small-scale hunter-gatherers settled agriculturalists began to produce more goods, as specialization took root. Pottery was one of the primary inventions of the past 10,000 years which transformed human life, and to a great extent defined village society as we understand it until recently. And because of its abundance and robustness to total destruction, it serves as a critical window upon the material culture of most ancient societies, literate or not.

Ancient Roman pottery is a clue as to fashions and economic vitality over the centuries.

But today it is not the only window upon the past. With powerful genetic technologies, one can reconstruct families and even narratives of particular parts of life, tragic as they might be. A new paper, Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave, illustrates the power of fine-grained genetic technologies operating in concert with classical forensic archaeology to flesh out the past in vivid detail.

The authors obtained DNA from many of the individuals in a Neolithic mass grave. The people were members of the Globular Amphora Culture (GAC), which was one of the last Neolithic societies in Northern Europe before the arrival of the steppe people. They were killed by blows to the head, and “the nature of the injuries…suggest that the individuals were captured and executed, rather than killed in hand-to-hand combat.”

This horrific scenario gains even greater pathos when the authors established genetic relationships between the individuals. From the paper:

Overall, we identified four nuclear families in the grave, which are for the most part represented by mothers and their children…Closely related kin were buried next to each other: a mother was buried cradling her child, and siblings were placed side by side. Evidently, these individuals were buried by people who knew them well and who carefully placed them in the grave according to familial relationships.
Interestingly, the older males/fathers are mostly missing from the grave, suggesting that it might have been them who buried their kin….

Obviously, it is not surprising that these are relatives. And the scenario that many members of the community, in particular, older males, were away from the village during the killings comports when what we know from ethnography in terms of the nature of these raids. But the relatedness inferred from genetics brings the narrative to life.

Prehistory will always be about pots. But more and more they will be about the relationships of people.


Anatomy of a prehistoric atrocity was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

May 7, 2019

Pleistocene rock art in Maharashtra

Filed under: Archaeology,History — Razib Khan @ 12:39 am

Ancient Rock Art in the Plains of India-Two amateur sleuths have uncovered a collection of mysterious rock carvings on the Indian coastal plain south of Mumbai:

In the evening breeze on a stony hilltop a day’s drive south of Mumbai, Sudhir Risbud tramped from one rock carving to another, pointing out the hull of a boat, birds, a shark, human figures and two life-size tigers.

“They’re male,” he said with a smile, noting that the carver had taken pains to make the genitalia too obvious to ignore. He was doing a brief tour of about two dozen figures, a sampling of 100 or so all etched into a hard, pitted rock called laterite that is common on the coastal plain that borders the Arabian Sea.

The carvings are only a sample of 1,200 figures that Mr. Risbud and Dhananjay Marathe, engineers and dedicated naturalists, have uncovered since they set out on a quest in 2012. The two men are part of a long tradition of amateur archaeologists, according to Tejas Garge, the head of the Directorate of Archaeology and Museums for the state of Maharashtra, and the petroglyphs they have uncovered amount to a trove of international significance.

There are no depictions of bulls, so it is pre-agricultural. Additionally, some of the animals depicted disappeared from the area in the later Pleistocene. That means the carvings could date to people who lived in the area between 40,000 and 20,000 years ago, right up to the Last Glacial Maximum.

April 3, 2019

Echoes of Europe’s Pleistocene Past

Filed under: Archaeology,Europe,Genetics,Ice Age,Uncategorized — Razib Khan @ 8:26 am
Lascaux Cave, 17,000-year-old Magdalenian “paintings”

40,000 years ago the first modern humans arrived in Europe. They were the scions of a great scattering of Africans. One branch of the “Out of Africa” migration, from which the vast majority of the ancestry of modern peoples derive. These early modern humans were responsible for the cave paintings which are among the oldest works of art known from our species. Their cultural impact is powerful and has shaped our conceptions of the past for the past few centuries, as we’ve begun to develop an antiquarian interest as a species.

Moderns vs. Neanderthals

And yet it is notable that modern humans arrived in Europe thousands of years after they settled Australia. This, despite Europe being much closer to Africa than Australia as a simple matter of geography.

A straightforward explanation for the relatively late settlement of modern humans in Europe is that they were not the only humans present in Eurasia during their expansion out of Africa (in contrast to Australia, where placental mammals aside from bats were nearly nonexistent before the arrival of our species). Neanderthals had occupied the whole zone between the Atlantic and the Altai in a broad high latitude belt for hundreds of thousands of years, with their Denisovan cousins ranging further east.

Jebel Irhoud fossil from North Africa is 300,000 years old and exhibits proto-modern features

In the Near East, Neanderthals seem to have moved south during colder periods, as African-related humans retreated, with the dynamic reversing during warmer periods. Anatomically modern humans, people with more delicate skulls and flatter faces, had been present in Africa for hundreds of thousands of years while the Neanderthals flourished to their north.

But the coexistence was not to last.

Something different happened 40,000 years ago. A few thousand years after the arrival of modern humans in Europe, the Neanderthals disappeared from the fossil record. In the last decades of the 20th-century, the dominant view was that the Neanderthals had been marginalized or exterminated to extinction. They were an evolutionary dead-end, and the humans who arrived 40,000 years ago were the ancestors of modern Europeans.

But with DNA, ancient and not so ancient, the truth turns out to be more complex than we had imagined. In 2010 researchers in Germany discovered that the ancient genome of the Neanderthals had left an imprint in all the peoples outside of Africa. From Europe to Australia to the Americas. The conclusion is clear: our African ancestors mixed with Neanderthals somewhere in the Middle East before they spread out across the world.

Yet modern Europeans actually have less Neanderthal ancestry than people from eastern Asia, despite the fact that Neanderthals were residents of Europe for hundreds of thousands of years.

These strange facts tell us the deep human past was not a straightforward process of replacement and settlement, but probably involved multiple migrations and mixtures. When the first genome of a 40,000-year-old modern human European was sequenced, the results surprised many people.

Bones at Peştera cu Oase

The remains were from Peştera cu Oase, in Romania. The individual was from an early Aurignacian culture. This is the first archaeological tradition in Europe associated with modern humans. The two primary genetic findings from the individual who died at Peştera cu Oase is that they do not seem to have left any descendants among modern Europeans, and, they had considerably more Neanderthal ancestry than modern Europeans.

In fact, this particular individual had a recent Neanderthal ancestor four to six generations earlier!

So the earliest modern humans in Europe mixed with local Neanderthals, but also seem to have left no descendants today.

40,000-year-old Lion Man from Germany

Because of Europe’s historical support for archaeological research, and the reality that the cool climate is optimal for preservation of remains and artifacts, the European Upper Paleolithic is well defined by many cultures with familiar names. Aurignacian, Gravettian, Solutrean, and Magdalenian. These are just a few of the cultures which are well known to us from copious remains and objects.

These societies have served as the basis of popular cultural representations, from the Aurignacian people in The Clan of the Cave Bear to the Magdalenian tribe depicted in the 2018 film Alpha. If the Neanderthals represent one source of the archetype for “cavemen”, then these Ice Age European cultures represent another.

Citation: The genetic history of Ice Age Europe

Now, over the past decade, geneticists have assembled a European temporal transect of samples from the period between 40,000 and 10,000 years ago. The whole period of the Upper Paleolithic occupation of Europe by modern humans. What they have confirmed is that Pleistocene Europe was defined by population turnovers and mixtures, which reshaped Europe’s genetic landscape several times across the Ice Age. This was not a static time, but a dynamic one.

The European hunter-gatherers who were indigenous to the continent when farmers arrived from the Near East with the Neolithic Revolution were themselves relatively recent arrivals, expanding only after the Last Glacial Maximum.

Though only a small proportion of the ancestry of modern Europeans seems to date to these Pleistocene peoples, the ancestry of later Aurignacian cultures, as well as the Gravettian, Magdalenian, archaeological complexes, has left an impact on modern Europeans.

A Magdalenian artifact

The demographic history of Europe has been characterized by several repeated pulses of migration from the southeast and east. The earliest Aurignacians were replaced in totality, but the later ones seem to have been absorbed into the Gravettians, and also persisted in pockets across Western Europe, only to reemerge as one of the primary ancestral groups for the Magdalenian people. After the end of the Last Glacial Maximum, a final group of Pleistocene hunter-gatherers emigrated out of the fringes of Southeast Europe, the Near East, and the Caucasus, and assimilated the remnants of these earlier cultures.

It was this last wave of hunter-gatherers who eventually gave rise to the Mesolithic hunter-gatherers of Europe and also contributed to the ancestry of the first farmers in Anatolia, the Levant, and the Zagros.

The peoples of Ice Age Europe have left art which fascinates us to this day. Their efflorescence of creativity was such that the idea of “behavioral modernity” and the cognitive “great leap forward” arose to explain the new genius of our species. Now genetics now tells us that these early Europeans, who occupied the content for 30,000 years before the end of the Ice Age, left only a shadowy and faint imprint on present generations. In that way, they share a fate with the Neanderthals.

But the artistic legacy is something that will persist, haunting our imaginations. Though they may not be the ancestors of modern Europeans in a literal genealogical sense, through their works the influence of Pleistocene Europeans has persisted across the eons, and will continue to do so.


Echoes of Europe’s Pleistocene Past was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

February 20, 2019

The Insight Show Notes — Season 2, Episode 15: The Prehistory of the Arabian Peninsula

Filed under: Archaeology,oman,Out-of-Africa — Razib Khan @ 3:56 pm

The Insight Show Notes — Season 2, Episode 15: The Prehistory of the Arabian Peninsula

Dhofar, Oman, during the “wet season”

This week on The Insight (Apple Podcasts, Stitcher and Google Podcasts)we discuss the prehistory of the Arabian peninsula with archaeologist Dr. Jeffrey Rose. We range over tool technology, geology, and the relationship between language and genetics.

Watch him in action as he instructs students on how to identify stone tool-making techniques:

As Rose does much of his fieldwork on the Dhofar uplands of southern Oman, we reviewed the unique geography and history of this region. Located on the border with Yemen, Dhofar is subject to the monsoons and experiences a rainy season. Unlike the deserts to the north and the interior, this region of Oman shares more biogeographically within the African savannas than the temperate zones. Rose mentions that even organisms such as frogs and snails exhibit differences between Dhofar and the rest of Oman.

There was extensive discussion about the Nubian Complex of Dhofar. This is an archaeological culture which dates to the Middle Paleolithic and ties Africa to Arabia. This is important because it may help us trace the “Out of Africa” migration and concretely connects Africa to Arabia. In keeping with Dhofar’s uniqueness in the region, the Nubian Complex extends no further to the north and east. An outpost of Africa if you will.

We mentioned the “Green Arabia” theory, which posits that there were past periods when the aridity of the region was far less than what it is today.

Rose also discussed in detail the Levallois technique, a variant of which helps define the Nubian technology that is so distinctive and easy to trace.

There was a review of the ethnographic diversity of southern Arabia. In particular, the indigenous people of Dhofar, the Mehri, as well as various other “South Semitic” ethno-linguistic groups. Rose reminds us that Arabic was not traditionally the native language from Yemen to Oman, but rather was a recent introduction in historical times.

The closest languages to South Arabian dialects are to be across the Red Sea, in the highlands of Ethiopia. This highlights the fact that Rose’s work traces migrations out of Africa, but may also help flesh out migrations back into Africa.

We discussed the origins of the Sumerians in the Gulf region when the sea levels were much lower. Rose also alluded to the fact that Arab legends suggest that the people of southern Arabia were originally a very different group of agro-pastoralists.

Finally, Rose points to the genetic work of David Reich’s lab, and how their Middle Eastern work aligns with his own findings. We discuss “Basal Eurasians” and how they might relate to Arabian prehistory.

More videos of Dr. Jeffrey Rose:


The Insight Show Notes — Season 2, Episode 15: The Prehistory of the Arabian Peninsula was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

August 15, 2018

The Insight Show Notes: Episode 32, So you want to be a geneticist…

Filed under: anthropology,Archaeology,Genetics,science — Razib Khan @ 5:45 pm
Drosophila

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we talk to an “early career” geneticist, Austin Reynolds. A graduate of Indian University and University of Texas-Austin, he is currently a post-doctoral fellow at University of California-Davis.

Alfred H. Sturtevant in his own “fly lab”

As a field, genetics is officially a bit over a century old. Though Gregor Mendel made his key discoveries fifty years before. Since the year 2000 genetics has undergone a revolution driven by sequencing technology and more powerful computing. Around 2010, a different revolution began, which Austin has been a part of, involving the synthesis of archaeology and genetics with the field of ancient DNA.

The first ancient whole-genome analysis, Ancient human genome sequence of an extinct Palaeo-Eskimo. Also, the Neanderthal paper which revolutionized our understanding of our relation to this lineage.

An excellent review of the state of the current research, Ancient Human Genomics: The First Decade. And a preview of the future, Tales of Human Migration, Admixture, and Selection in Africa.

David Reich’s book Who We Are and How We Got Here is a good primer on ancient DNA and population genetics. Highly accessible to the lay audience without sacrificing any of the scientific content.

Loci associated with skin pigmentation identified in African populations.

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.

On career issues, Track the fate of postdocs to help the next generation of scientists.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The Insight Show Notes: Episode 32, So you want to be a geneticist… was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

August 9, 2018

The new post-genetic paradigm will come

Filed under: Archaeology,History,Prehistory — Razib Khan @ 1:29 am

Oftentimes the domain on which a technical framework is applied matters a great deal. Imagine, if you will, an explicit statistical test for a phylogenetic relationship between a set of extant populations, whereby one infers a group of ancestral populations. If the genus is Drosophila, it’s academic. Interesting, but academic. If the genus is Homo, then it gets complicated.

People care a great deal about the historical inferences made from human population genomic datasets. I say genomic, and not genetic, because the last ten years with genome-wide analyses and ancient DNA is very different from what we saw in the late 20th century and aughts. The definitive granularity is such that population genomics has touched upon very sensitive and precious issues, both in a scholarly and non-scholarly context.

A lot of the time I have my head down reading supplements where the statistical methods are. The reality is that this sort of science is cutting edge, and there are always later revisions. Usually you can see where those revisions might come from if you look at the detailed methods and conclusions that are found in the supplements. Also, you will find that that is where you see the limitations, and the reasons that the authors chose particular parameters.

To give you a sense of what I’m talking about, consider 2016’s Genomic insights into the origin of farming in the ancient Near East. The paper proper is 24 pages. But the supplemental text is 148 pages. There is a lot of interesting stuff in there, but I would just jump to page 125 and read the whole section there and down to the end. The method portion is important because you always need to take number values in results with a grain of salt. You see for example later work which refines fractions significantly when it comes to estimating admixture between a finite set of putative populations. And the last section seems likely to become a paper in and of itself at some point

But that doesn’t mean that the genetic inferences are not robust and come out of a vacuum. In the details the phylogenetic models being tested are going to be wrong on many particulars, but in relation to hypotheses being tested they are often entirely sufficient to reject to accept.

For example, there was long the idea that the Basque people of the western trans-Pyrenees region of Spain and France descended from pre-farming Europeans, and therefore the Basque language, which is an isolate, might have local roots which went back to the Pleistocene. Today, ancient DNA along with explicit testing of various phylogenetic scenarios makes it clear that the largest fraction of Basque ancestry derives from “Early European Farmers,” who represent a demographic pulse which radiated out of the Eastern Mediterranean and reached Spain 7,500 years ago. Of course Basques do have local hunter-gatherer ancestry, but these Mesolithic peoples themselves were the last in a sequence of very distinctive populations in Pleistocene Europe. Finally, Basques do have admixture from Indo-European peoples, just less than other people in Iberia.

Of course, genetics can’t tell us about languages. Using linguistic labels in population genetic papers is to some extent a lexical convenience, but it is also one we use because of the constellation of information we have. The last major demographic pulse into Iberia is associated with an ancestry which derives from Central Eurasia. This ancestry is copious in Northern Europe, but is also found in South Asia, and ancient DNA suggests its expansion occurred between 5,000 and 3,500 years ago. It also happens that the Indo-European languages are spoken in both India and Europe. The natural inference then is to make an association between this language family, and this demographic pulse.

Some observers note discordance between estimated fractions from paper to paper, but don’t seem to understand that the point isn’t to estimate fractions of ancestry as ends in and of themselves, but to estimate fractions of ancestry to expose and highlight demographic change (or lack thereof). We can say with a very high degree of certainty that the period between 3000 and 2000 BC witnessed massive demographic change in Northern Europe. Somewhat later there was a similar change in Southern Europe, but more demographically modest. These are simple facts.

There are some scholars, frankly often archaeologists, who dismiss the relevance of the genetic findings. But anyone who has read archaeology knows that there are many cases where researchers see demographic continuity, and posit in situ cultural evolution, where it is just as possible that a new people arrived. The reason ancient DNA has revolutionized our understanding of prehistory isn’t because it has brought us new knowledge, it has foregrounded old and buried knowledge. The knowledge being that migration matters.

But genetics is only a skeleton. A framework. True flesh on the bones of the story needs the input of archaeologists, linguistics, and other scholars. In Who We Are and How We Got Here David Reich expresses his ambition to construct a historical genetic atlas of the world. But that atlas will be all the poorer without the input from other fields besides genetics. Many archaeologists have gotten on board with genetics as a tool, but the reality is that there needs to occur the rejection of some theories precious to some scholars if there is going to be total buy-in. Eventually that will happen, and a new synthesis will arise.

March 2, 2018

Do the Amerindians descend from Southeast Asians?

Filed under: Archaeology,Native Americans — Razib Khan @ 12:03 am

Many people have recommended I read Johanna Nichols’ Linguistic Diversity in Space and Time over the years. I checked out the book in grad school once but didn’t get around to reading it. But today I see it being referenced in Stephen Oppenheimer’s very strange book about Lemuria-I mean Southeast Asia, Eden in the East.

Both of these books were written in the late 1990s, before the current swell of genome-wide and ancient DNA analysis. Oppenheimer reports Nichols’ comparative analysis of linguistics implies that the ancestors of the Amerindians were not interior Siberians, but coastal people who came up from Southeast Asia.

Today we know this is somewhat wrong. About 30 to 40 percent of the ancestry of modern Native Americans derives from Ancient North Eurasians, who seem to be most commonly found in the great Eurasian heartland, probably to the east of what we think of today as Europe, but west of the Pacific.

But there’s more. Most of the ancestry of Native American peoples seems to be more like that of East Asians. Today this component extends rather far north, into Korea, Japan, and such. But these are consequences of recent demographic movements. Nichols’ Southeast Asian hypothesis may actually not be off-base, in particular in light of other evidence suggesting admixture with an Australo-Melanesian population.

One of the major issues with the field of ancient DNA and the historical inferences people make is that the theories and models are often quite ad hoc, and emerge in response to the data. But these earlier ideas, informed by linguistics and archaeology, are actually a pretty good source of possible ideas. They may not be constrained by genetics, because we didn’t have that information (aside from mtDNA), but are richly informed by other disciplines.

 

November 10, 2017

Before the Indo-Europeans in Ukraine

Filed under: Archaeology — Razib Khan @ 6:00 pm

It’s been ten years since I read The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. It’s a great book, but some of the material was very wrong. The author, David Anthony, helped provide samples which undercut his thesis that Indo-Europeanization in Europe was mostly a matter of elite cultural diffusion. Rather, it looks as if there was a massive migration from the steppes.

The Horse, the Wheel, and Language was heavy on archaeology which I found hard to follow. The Cucuteni–Trypillia culture plays a major role in the narrative since it seems to have been a source of cultural influence on the Yamnaya steppe culture which eventually overran it. A new preprint seems to confirm that there was a genetic discontinuity. Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture

…Burials at Verteba Cave are largely commingled and secondary in nature. A total of 68 individual bone specimens were analyzed. Most of these specimens were found in association with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do not suggest continuity with local pre-Eneolithic peoples, but rather complete population replacement. We constructed maximum parsimonious networks from the data and generated population genetic statistics…We find different signatures of demographic expansion for the Tripolye people that may be caused by existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of the Tripolye Culture are more closely related to early European farmers and lack genetic continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.

There is stuff in the preprint about population expansion. My personal opinion is that in most cases genetics doesn’t add much beyond what archaeology does for humans in reconstructing population history. Rather, these results in concern with others are strongly indicative of population turnover. Uniparental lineages are still useful, but only in the context of other data.

The great thing about genetics when it is so clear and striking is that it clears up confusions about relationships in the past that otherwise would be unclear. It’s like having a time machine. So we now know that early European farmers (EEF). Over the next decade or so we’ll get a really granular understanding of the ebb and flow of populations across prehistoric and historic Europe. This won’t abolish all controversy, but it will reduce the space of the unknown….

August 12, 2017

The revolution which came to archaeology without archaeologists?

Filed under: Archaeology,Mycenaeans — Razib Khan @ 1:29 pm

The recent letter to Nature, Genetic origins of the Minoans and Mycenaeans, has elicited some response from those outside of genetics. The first author of the paper linked to these two, Who are you calling Mycenaean? and On genetics and the Aegean Bronze Age.

One of the common elements to both reactions was that the paper’s definition, or reification, of Mycenaean and Minoan constructs was naive. From one of the posts:

In a press interview following the publication of the study, one of the main authors claimed that ‘there is no doubt that our findings reflect historical events in the Greek lands’: ‘the picture of historical continuity is crystal clear, as is very clear the fact that through the centuries Greeks evolved receiving genetic influences from other populations.’ The category of ‘Greekness’ here appears more or less given and stable, despite the ‘influences’, from the Early Bronze Age to the present. It sounds like a version of the 19th-century national narrative of the power of eternal Hellenism to absorb external influences.

Context is important here. The last ten years have seen a massive updating of our assumptions about the nature of demographic change in the pre-modern world. Geneticists using ancient DNA have been central to this process. They’ve overturned a lot of archaeological orthodoxies.

One of the major assumptions seemingly at the heart of the two critical posts is that modern ideas of nationhood were a recent construction. The stylized assertion is that modern nationalism begins with the French Revolution. To me this is like the assertion that the troubadours invented romantic love during the High Middle Ages. While it is true that the troubadours popularized a particular form of romantic love, the core emotional impulses are primal, and didn’t need “inventing.” Similarly, ideas of nationality are clearly primal, because they derive from the tribal structures of prehistoric humanity. Tribes are an evoked part of human culture. That is, given similar cognitive hardware, the same software seems to get installed for the same tasks (group cohesion and inter-group competition).

Ironically, the period between the “rise of civilization” and the modern era may have been one defined by the regression of nationalistic thinking, because tribalism had to be suppressed with the rise of multiethnic agricultural states. Only with early modern information technology, and the spread of a literate middle class culture united by common mores and touchstones, could primal tribalism be transformed into modern nationalism (to this way of thinking it is not a coincidence that German nationalism with the Lutheran Reformation was supercharged by the arrival of the printing press).

Peter Heather in Empires and Barbarians and Azar Gat in Nations outline the revisionist views I’m alluding to in regards to the ancient origins of nationalism. But from a perspective of a geneticist the very high differentiation between nearby groups that persist for hundreds and even thousands of years is indicative of high levels of cultural distinction and consciousness (because only small amounts of gene flow between groups is enough to eliminate differences very rapidly). Genetics can’t maintain these sorts of differences, only strong cultural ideologies can.

Finally, quoting from the same post:

First, there’s not much new here. I mean, the data are new, but the conclusions are largely consistent with the archaeological consensus: there’s no big genetic difference between “Minoans” (Late Bronze Age Cretans) and “Mycenaeans” (Late Bronze Age inhabitants of the Greek mainland), and both are pretty close genetically to Late Bronze Age southwestern Anatolians….

The archaeological consensus was correct here to a great extent. But in other areas it has not been right of late. That’s why it is not so ho-hum. In The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe the authors show that:

1) the spread of Beaker culture from Southwest Europe to Central Europe was one of cultural transmission (archaeologists would not be surprised).

2) the spread of Beaker culture to England from Central Europe was one of demographic replacement on the order of 90% over a few hundred years (archaeologists would be surprised).

It’s easy for archaeologists to be surprised that geneticist are presenting ideas that they “refuted” in the 1960s. But it turns out that the predictions on a demographic scale are easily refuted in many places and times by genetics. The issue isn’t whether it’s pots or peoples, but what the mix of pots and people are. This research is part of a broad program of nailing down the values in these parameters, as opposed to simply going along with archaeological orthodoxy.

November 20, 2013

Our ancestors are part us…or the other way around?

Filed under: Archaeology,Siberian boy — Razib Khan @ 11:34 am

Keeping a close watch on media representations of the new Nature paper on the ancient Siberian genome. Here’s The New York Times, 24,000-Year-Old Body Is Kin to Both Europeans and American Indians. I don’t have a problem with the title, but the roll-out isn’t totally accurate in what it will connote to the audience in my opinion:

he genome of a young boy buried at Mal’ta near Lake Baikal in eastern Siberia some 24,000 years ago has turned Tout to hold two surprises for anthropologists.

The first is that the boy’s DNA matches that of Western Europeans, showing that during the last Ice Age people from Europe had reached farther east across Eurasia than previously supposed. Though none of the Mal’ta boy’s skin or hair survive, his genes suggest he would have had brown hair, brown eyes and freckled skin.

The second surprise is that his DNA also matches a large proportion — some 25 percent — of the DNA of living Native Americans. The first people to arrive in the Americas have long been assumed to have descended from Siberian populations related to East Asians. It now seems that they may be a mixture between the Western Europeans who had reached Siberia and an East Asian population.

The Mal’ta boy was aged 3 to 4 and was buried under a stone slab wearing an ivory diadem, a bead necklace and a bird-shaped pendant. Elsewhere at the same site some 30 Venus figurines were found of the kind produced by the Upper Paleolithic cultures of Europe. The remains were excavated by Russian archaeologists over a 20-year period ending in 1958 and stored in museums in St. Petersburg.

The issue I have is that modern Europeans are a new population which emerged through admixture processes over the past ~10,000 years. And one of those populations which contributed to their ancestry are the descendants of the Siberian boy! Talking about “Western Europeans” ~20,000 years ago is geographic convenience. They wouldn’t be “Western Europeans” as we understand them genetically. Even if there wasn’t any recent admixture, ~1,000 generations of drift is not trivial. Though the archaeology may clarify, I also don’t think it is definite that the ancient Siberians were from Europe as we’d understand it. Perhaps they all come from a common Central Eurasian stock which diversified?

Not that I have a better solution for terminology.

The post Our ancestors are part us…or the other way around? appeared first on Gene Expression.

The long First Age of mankind

Filed under: Anthroplogy,Archaeology,Siberians — Razib Khan @ 10:22 am

OldSiberian

“What it begins to suggest is that we’re looking at a ‘Lord of the Rings’-type world – that there were many hominid populations,” says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

- Mark Thomas, as reported by Nature

This is in reference to the ancient DNA meeting where David Reich reported that the Denisovans, an exotic archaic population which contributed ~5-10 percent of the ancestry of Papuans, was itself a synthesis of Neandertals and a mysterious group currently unknown. This is not surprising, as the broad outlines of these results were presented at ASHG 2012, though no doubt they’re moving closer to publication. But for this post I want to shift the focus to a different time and place, after the ancient admixture with archaic lineages, and to the reticulation present within our own.


But first we need to backtrack a bit. Let’s think about what we knew in the early 2000s. If you want a refresher, you might check our Spencer Wells’ The Journey of Man or Stephen Oppeneheimer’s Out of Eden, which focused on Y and mtDNA lineages respectively. These books were capstones to the era of uniparental phylogeographic analysis of the spread and diversification of anatomically modern African hominids ~50-100,000 years ago. Rather than looking at the whole genome (the technology was not there yet) these researchers focused on pieces of DNA passed down via direct maternal or paternal lineages, and reconstructed clean phylogenetic trees using a coalescent framework. Broadly speaking these trees were concordant, and told us that our lineage, all extant humans, derived from a small African population which flourished ~100,000 years ago. These insights suffused the thought of human evolutionary thinkers in other disciplines (see The Dawn of Human Culture). H. sapiens sapiens, veni, vidi, vici.

After that initial “Out of Africa” migration a series of bottlenecks and founder events led to the expansion of our lineage, as it replaced all predecessors. By the Last Glacial Maximum, ~20-25,000 years ago, the rough outlines of human genetic variation were established (with the exception of the expansion into the New World). We know now that this picture is very incomplete at the most innocuous, and highly misleading given the least charitable interpretation.

Reticulation. Graphs. Admixture. These words all point to the reality that rather than being the culmination of deep rooted regional populations which date back to the depths of the Pleistocene, most modern humans are recombinations of ancient lineages. On the grandest scale this is illustrated by the evidence of ‘archaic’ ancestry in modern humans. But even more pervasively we see evidence of widespread admixture between distinct lineages which are major world populations which we think of as archetypes. This is true for Amerindians, South Asians, and Europeans. This is also the case for Ethiopians, and Australian populations. A major problem crops up when we talk about extinct ancient populations which were the founding substituent elements of modern ones: it doesn’t make sense to use modern referents when they are simply recombinations of what they are describing. But language and history being what they weare we can’t change the awkwardness of talking about “Ancestral North Eurasians,” anodyne and somewhat incoherent at the same time (Eurasia is a modern construct with contemporary historical salience).

Into the mix comes another ancient DNA paper which reconstructs the genome of a boy who lived in Siberia, near Lake Baikal, somewhat over 20,000 years ago. It’s titled Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Here’s the topline finding: a substantial minority of the ancestry of modern Native Americans derives from a North Eurasian population which has closer affinities to West Eurasians than East Eurasians. And, this is an old admixture event. In the paper itself they observe that all “First American” populations seem to exhibit the same admixture distance to the Siberian genome. These results are also broadly consistent with the admixture of this population in Western Eurasia, especially northeast Europe. As among Amerindian populations it seems that this element is at substantial minority across Europe as a whole, and perhaps at parity in some populations, such as Finns.

Fig1To the left you see the geographical affinities of the MA-1 Siberian sample. It is shifted toward West Eurasians in the PCA. But on the map with circles representing populations, the definite evidence of admixture between Amerindians and MA-1 is clear in the shading. The statistic used, f-3, looks for complex population history between and outgroup (X) and a putative clade. From this test it is evident Amerindians had some admixture related to MA-1. Because of the dating of Siberian remains it does not seem likely that admixture was from Amerindians to West Eurasian and related populations. Rather, the reverse seems more plausible. You can also see from the map the close affinities with particular European and Central Asian populations of MA-1. This is intriguing, and requires further follow up. Though MA-1 and its kin were closer to West Eurasians than East Eurasians, it still seems likely that there was an early divergence between the populations of north-northeast Eurasia, and those of the southwest. Eventually they came back together in various proportions to produce modern Europeans, but it seems likely that during the Pleistocene these two groups went their own way.

treemixThere are hints of this in the TreeMix plot to the right. Note now drifted MA-1 is in relation to other West Eurasians (the branch is long). I suspect some of this is due to the fact that this individual is nearly 1,000 generations in the past. Not only is it difficult to name ancient populations with those of moderns, I suspect that some of the variation in the ancient populations has been lost, and so they seem exotic and difficult to fit into a broader phylogenetic framework (they had hundreds of thousands of SNPs though). And yet MA-1 can be fitted into the broader framework of populations which went north or west after leaving Africa because of mtDNA and Y chromosome results. Both of these indicate that MA-1 was basal to West Eurasians, with haplogroup U for mtDNA, and R for the Y lineage.

To really understand what’s going on here is going to take a while. A later subfossil, circa ~15,000 years before the present, yielded some genetic material, and exhibited continuity with MA-1. This suggests that Siberia may have had massive population replacement relatively recently. We know this was likely the case elsewhere. Reading Jean Manco’s Ancestral Journeys one possible scenario is that Pleistocene Europeans were MA-1 like, but were replaced by Middle Eastern farmers in the early Neolithic. But later eruptions from Central Asia brought mixed populations (Indo-Europeans?) with substantial MA-1 affinities to the center of European history.

Finally, one must make a note of phenotype. The authors looked at 124 pigmentation related SNPs (see supplemental). The conclusion seems to be that MA-1 was not highly de-pigmented, as is the case with most modern Northern Europeans. This stands to some reason, as substantial ancestry of this sort in Amerindians would result in phenotypic variation which does not seem to be present. Though the authors do suggest that coarse morphological variation among early First Americans (e.g., Kennewick Man) might be due to this population, which had West Eurasian affinities.

Where does this leave us? More questions of course. Though I’m confident the befuddlement will clear up in a few years….

Citation: doi:10.1038/nature12736

Addendum: Please read the supplements. They’re rich enough that you don’t need to read the letter if you don’t have access. Also, can we now finally bury the debate when east and west Eurasians diverged? Obviously it can’t have been that recent if a >20,000 year old individual had closer affinity to western populations.

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October 30, 2013

The human genetic casserole

Filed under: Archaeology,Human History — Razib Khan @ 6:48 pm

HotdishI haven’t said much about this article in Science, Ancient DNA Links Native Americans With Europe, because it would be an understatement to say I’m digesting it. I would offer up a caution that using terms like “Europeans” and “East Asians” for populations which flourished ~25,000 years ago might be misleading. We are used to thinking of genetic distance in terms of space, but time is also a dimension to consider. Populations even without admixture or gene flow will have drifted in allele frequencies over so many generations.

But I have to admit that it seems more and more likely that most extant modern populations are combinations of lineages which diverged very early after the “Out of Africa” migration. We see this clearly with South Asians, and now Europeans and Native Americans. The Reich lab has also found evidence of admixture in in Australians. The closer we look, the more amalgamation we see between disparate lineages. Using the elements of the present to reconstruct the patterns of the past is going to be a more daunting task than most would have guessed.

The post The human genetic casserole appeared first on Gene Expression.

November 17, 2012

The archaeologist, James Fallows, and Neandertals

Filed under: Anthroplogy,Archaeology,Genetics,Neandertals — Razib Khan @ 10:10 pm

A month ago I posted Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology, in response to James Fallows at At 5% Neanderthal, You Are an Outlier. Fallows has now put up a follow up, The Neanderthal Defense Committee Swings Into Action, where he links to my response post. This prompted the original archaeologist in question to reach out to me via email. I am posting the letter, with their permission, below.

Hello!

I’m dropping an email because I followed a link from Fallows to find my email to him highlighted negatively on your blog. I’ve emailed a few times with Mr. Fallows on various topics and had no idea he was going to post that email – he didn’t ask until after it was already up and so, yes you’re right it was a casual dashed off email and confused two different articles (both of which incidentally I have read so please no more comments on what I may or may not have done). Mea Culpa. And you’re right, I’m not a geneticist – I’m not even a lab scientist. However, I know a heck of a lot about archaeology and I work closely with ...

July 12, 2012

The past as a cultural landscape

Filed under: Anthroplogy,Archaeology,Native Americans — Razib Khan @ 9:03 pm

By now you have read that the Clovis people may have had contemporaries. In case you didn’t know, until about ~10 years the “standard model” of the peopling of the Americas was that around ~13,000 years ago one single population crossed into the New World via Beringia, and rapidly swept north to south in ~1,000 years. These were the Clovis people, associated with a particular toolkit, and perhaps implicated in megafaunal extinctions. Today this model is no longer held to be sacrosanct, though no clear successor has emerged. It does seem likely that some sort of pre-Clovis population is presumed to exist. These data are interesting because they indicate that there may have been geographical structure in cultural forms even at this early stage in North America, implying that the original peopling of America was not homogeneous. That is, there may have been several founding groups.

I find this entirely plausible. It strikes me that a fear years ago a tendency toward rhetorical extremism occasionally found purchase when it came to the settlement of the peripheries of the human range, Oceania and the New World. Jared Diamond famously proposed that ...

May 15, 2011

Genetic variation in the Caucasus

The Pith: There is a very tight correlation between language and genes in the Caucasus region.

If the Soviet Union was the “The Prisonhouse of Nations,” then the Caucasus region must be the refuge of the languages. Not only is this region linguistically diverse on a fine-grained scale, but there are multiple broader language families which are found nowhere else in the world. The widespread Indo-European languages are represented by Armenians, Greeks, and Iranians. The similarly expansive Altaic languages are represented by the Turkic dialects. But in addition to these well known groups which span Eurasia there are the Northwest Caucasian, Northeast Caucasian, and Kartvelian, families. These have only a local distribution despite their distinctiveness.

On the one hand we probably shouldn’t be that surprised by the prominence of small and diverse language families in this rugged region between Russia and the Near East. Mountains often serve as the last refuges of peoples and cultures being submerged elsewhere. For example, in the mountains of northern Pakistan you have the linguistic isolate of Burusho, which has no known affinity with other languages. Likely it once had relatives, but they were assimilated, leaving only ...

February 2, 2011

Empires and Barbarians: The Fall of Rome and the Birth of Europe

Link to review: Say it with me: Völkerwanderung

December 13, 2010

Live not by visualization alone

pc1
Synthetic map

In the age of 500,000 SNP studies of genetic variation across dozens of populations obviously we’re a bit beyond lists of ABO blood frequencies. There’s no real way that a conventional human is going to be able to discern patterns of correlated allele frequency variations which point to between population genetic differences on this scale of marker density. So you rely on techniques which extract the general patterns out of the data, and present them to you in a human-comprehensible format. But, there’s an unfortunate tendency for humans to imbue the products of technique with a particular authority which they always should not have.

ResearchBlogging.orgThe History and Geography of Human Genes is arguably the most important historical genetics work of the past generation. It has surely influenced many within the field of genetics, and because of its voluminous elegant visual displays of genetic data it is also a primary source for those outside of genetics to make sense of phylogenetic relations between human populations. And yet one aspect of this great work which never caught on was the utilization of “synthetic maps” to visualize components of genetic variation between populations. This may have been fortuitous, a few years ago a paper was published, Interpreting principal components analyses of spatial population genetic variation, which suggested that the gradients you see on the map above may be artifacts:

Nearly 30 years ago, Cavalli-Sforza et al. pioneered the use of principal component analysis (PCA) in population genetics and used PCA to produce maps summarizing human genetic variation across continental regions. They interpreted gradient and wave patterns in these maps as signatures of specific migration events. These interpretations have been controversial, but influential, and the use of PCA has become widespread in analysis of population genetics data. However, the behavior of PCA for genetic data showing continuous spatial variation, such as might exist within human continental groups, has been less well characterized. Here, we find that gradients and waves observed in Cavalli-Sforza et al.’s maps resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns do not necessarily reflect specific migration events. Our findings aid interpretation of PCA results and suggest how PCA can help correct for continuous population structure in association studies.

A paper earlier this year took the earlier work further and used a series of simulations to show how the nature of the gradients varied. In light of recent preoccupations the results are of interest. Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture:

In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East ∼10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the “allele surfing” phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion.

The first figure shows the general framework with which they performed the simulations:

pcab1

You have a lattice which consists of demes, population units, all across Europe. They modulated parameters such as population growth (r), carrying capacity (C), and migration (m). Additionally, they had various scenarios of expansion from the southwest or southeast, as well as two expansions one after another to mimic the re-population of Europe after the Ice Age by Paleolithic groups, and their later replacement by Neolithic groups. They modulated admixture and introgression of genes from the Paleolithic group to the Neolithics so that you had the full range where the final European were mostly Neolithic or mostly Paleolithic.

Below are some of the figures which show the results:

allesurAs you can see the strange thing is that in some models the synthetic map gradient is rotated 90 degrees from the axis of demographic expansion! In this telling the famous synthetic map showing Neolithic expansion might be showing expansion from Iberia. Perhaps a radiation from a post-Ice Age southern refuge?

One explanation might be “allele surfing” on the demographic “wave of advance.” Basically as a population expands very rapidly stochastic forces such as random genetic drift and bottlenecks could produce diversification along the edge of the population wave front. The reason for this is that these rapidly expanding populations explode out of serial bottlenecks and demographic expansions, which will produce genetic distinctiveness among the many differentiated demes bubbling along the edge of expansion. Alleles which may have been at low frequency in the ancestral population can “fix” in descendant populations on the edge of the demographic wave of advance. This is the explanation, more or less, that one group gave last year for the very high frequencies of R1b1b2 in Western Europe. With this, they overturned the classic assumption that R1b1b2 was a Paleolithic marker, and suggested it was a Neolithic one.

Here’s their conclusion from the paper:

A previous study showed that the original patterns observed in PCA might not reflect any expansion events (Novembre and Stephens 2008). Here, we find that under very general conditions, the pattern of molecular diversity produced by an expansion may be different than what was expected in the literature. In particular, we find conditions where an expansion of Neolithic farmers from the southeast produces a greatest axis of differentiation running from the southwest to the northeast. This surprising result is seemingly due to allele surfing leading to sectors that create differentiation perpendicular to the expansion axis. Although a lot of our results can be explained by the surfing phenomenon, some interesting questions remain open. For example, the phase transition observed for relatively small admixture rates between Paleolithic resident and Neolithic migrant populations occurs at a value that is dependent on our simulation settings, and further investigations would be needed to better characterize this critical value as a function of all the model parameters. Another unsolved question is to know why the patterns generally observed in PC2 maps for our simulation settings sometimes arise in PC1 maps instead. These unexplained examples remind us that PCA is summarizing patterns of variation in the sample due to multiple factors (ancestral expansions and admixture, ongoing limited migration, habitat boundary effects, and the spatial distribution of samples). In complex models such as our expansion models with admixture in Europe, it may be difficult to tease apart what processes give rise to any particular PCA pattern. Our study emphasizes that PC (and AM) should be viewed as tools for exploring the data but that the reverse process of interpreting PC and AM maps in terms of past routes of migration remains a complicated exercise. Additional analyses—with more explicit demographic models—are more than ever essential to discriminate between multiple explanations available for the patterns observed in PC and AM maps. We speculate that methods exploiting the signature of alleles that have undergone surfing may be a powerful approach to study range expansions.

What’s the big picture here? In the textbook Human Evolutionary Genetics it is asserted that synthetic maps never became very popular compared to PCA itself. I think this is correct. But, the original synthetic maps have become prominent for many outside of genetics. They figure in Peter Bellwood’s First Farmers, and are taken as a given by many pre-historians, such as Colin Renfrew. And yet a reliance on these sorts of tools must not be blind to the reality that the more layers of abstraction you put between your perception and comprehension of concrete reality, the more likely you are to be led astray by quirks and biases of method.

In this case I do think first-order intuition would tell us that synthetic maps which display PCs would be showing gradients as a function of demographic pulses. And yet the intuition may not be right, and with the overturning of old orthodoxies in the past generation of inferences from the variation patterns in modern populations, we should be very cautious.

Citation: Olivier François, Mathias Currat, Nicolas Ray, Eunjung Han, Laurent Excoffier, & John Novembre (2010). Principal Component Analysis under Population Genetic
Models of Range Expansion and Admixture Mol Biol Evol

December 3, 2010

The great northern culture war

A new paper in The New Journal of Physics shows that a relatively simple mathematical model can explain the rate of expansion of agriculture across Europe, Anisotropic dispersion, space competition and the slowdown of the Neolithic transition:

The front speed of the Neolithic (farmer) spread in Europe decreased as it reached Northern latitudes, where the Mesolithic (hunter-gatherer) population density was higher. Here, we describe a reaction–diffusion model with (i) an anisotropic dispersion kernel depending on the Mesolithic population density gradient and (ii) a modified population growth equation. Both effects are related to the space available for the Neolithic population. The model is able to explain the slowdown of the Neolithic front as observed from archaeological data

The paper is open access, so if you want more of this:
fareq

Just click through above. Rather, I am curious more about their nice visualization of the archaeological data:


euroneolithic

Note how much variance there is in terms of the rate of change of the clines. As I’ve observed before there was a “break out” of the LBK farmers into Central Europe nearly 7,000 years ago, but it took much longer to close the gap between the farms on the frontier and the sea. This is well known from the archaeology, as there seems to have been a pause of ~1,000 years across much of the north European plain. On the scale of 10,000 years that’s not much time, but that’s about 40 generations. In Frisia it looks like the spreading of farming stopped for nearly ~2000 years!

Why the abatement of the spread of farming? I think the authors of the above paper are correct in their acceptance of the conventional wisdom of greater Mesolithic densities in Northern Europe. But I think perhaps a better description might be maritime Northern Europe. We often imagine early farmers displacing hunters and gatherers of game and herb, but what if in much of the world the main clash numerically was between dense populations oriented toward the sea, and those who were depended on the land? About seven years ago a study came out which argued for a rapid transition from seafood to meat in the diets of early Britons, Why Did Ancient Britons Stop Eating Fish?:

When cattle, sheep, pigs, and wheat arrived on the shores of Great Britain about 5,000 years ago, fish quickly fell off the Neolithic menu, according to an analysis of human bones scattered throughout the island.

“Farming really took off in Britain during the Neolithic. The main questions concerning the speed of change relates to how quickly Mesolithic peoples adapted—or otherwise—to the new farming methods and/or the spread of farming into Britain by new farming communities,” he said.

The research by Richards and colleagues Rick Schulting at Queen’s University Belfast and Robert Hedges at the University of Oxford tracks the shift in diet by examining the dietary signature stored in the bones.

They find that the shift was rapid and complete at the onset of the Neolithic. “Marine foods, for whatever reason, seem to have been comprehensively abandoned,” the researchers conclude in the September 25 issue of the journalNature.

“We determined that after the introduction of domesticates, as well as the other artifacts associated with the Neolithic, the isotope values showed that marine foods were not used anymore,” he said. “We then infer that this is a switch from wild foods such as fish and shellfish to the new domesticates that arrive at this time.”

Richards said there are three plausible reasons why the British abandoned seafood from the beginning of the Neolithic: the domesticated plants and animals presented a steady source of food; the shift was forced by a climate change; or cultural pressure.

In the early 2000s the idea of wholesale rapid demographic replacement was not in the air. I think we need to put that back on the table. Here is the chart on isotope ratios from the 2003 paper:
culwar

Notice the sharp discontinuity. Richards et al. in 2003 interpreted this as a rapid cultural acquisition of the Neolithic lifestyle ~2500-3000 BC. They note in the media reports that later Britons, for example at the time of the Roman conquest, seem to have utilized fish a bit more in their diet than these early Neolithics. This stands to reason, much of Britain is not too far from the sea. To me the very sharp drop in marine consumption is indicative more of a food taboo, than a practical shift. Obviously farmers would primarily be subsistent on grain, but there’s no necessary reason to avoid meat or fish, but as it happens in many parts of the world societies preserve and perpetuate exactly such norms. These norms may have spread through cultural diffusion, for example through an adoption of a new religion. Or, the norms may have been brought by a new group which arrived in large numbers and replaced the indigenous population.

Here is an equivalent chart from Denmark from an earlier paper by the same group:

denmark

800px-Saami_Family_1900pacnortWhen we think of peoples who aren’t farmers, we often think of marginalized nomadic or semi-nomadic groups. Many of the remaining hunter-gatherers such as Bushmen, as well societies which supplement their conventional lifestyle with a lot of hunting & gathering, such as the indigenous peoples of Siberia or the Sami of northern Scandinavia, occupy territory which is simply not viable for conventional agriculture. But this was not so in the past. Before the farmers arrived the rich bottom-lands were occupied by hunters & gatherers, of fish, game, grain, and nuts. In certain ecologies, such as around productive estuaries one could imagine enormous aggregations of these peoples. Additionally, it seems likely that a sedentary lifestyle predates farming. A good contemporary analog for what ancient Northern Europe may have been like was the Pacific Northwest before the European settlement. These native tribes were relatively affluent because of the abundance of salmon runs, and engaged in lavish signalling, such as with their famous potlatches. Seeing as how there are Atlantic salmon runs in places like Norway and Scotland one can make even closer correspondences perhaps!

Stonehenge-GreenAs I have stated before just because we have no written records of this period, we can not assume that these were necessarily the fragmented and scattered “small-scale societies” which we’re familiar with today. There may have been ideologically motivated political coalitions and alliances which broke down along ethnic and cultural lines. In the paper above the authors argue that there is evidence that a climatic constraint, crops which do not have a good yield in cooler or warmer temperatures, is a weak hypothesis. If so I wonder if it is a bit too pat to simply model the dynamics as a diffusive “bottom up” process. Seems plausible enough for much of Europe where Mesolithic populations were thin on the ground because of local carrying capacity, but I suspect that the encounter between dense agglomerations of farmers and fishermen resulted in an inevitable ramp up of political integration and consolidation, as villages and tribes had to coordinate together because of a positive feedback loop of conflict.

Image Credit: Lordkinbote, Mactographer

November 9, 2010

European man of many faces: Cain vs. Abel

UE-1

When it comes to the synthesis of genetics and history we live an age of no definitive answers. L. L. Cavalli-Sforza’s Great Human Diasporas would come in for a major rewrite at this point. One of the areas which has been roiled the most within the past ten years has been the origin and propagation of the agricultural lifestyle across the European continent between 10,000-6,000 years before the present (starting in Europe’s southeast fringe a few thousand years after the origination of the Neolithic lifestyle in the Levant, and finally pushing into the southern Scandinavian peninsula only ~6,000 years ago). The reasons for this particular debate about the origin of the European are manifold. First, most scholars are of European ancestry, and some of the debates have roots going back a century. So a natural interest exists based on normal human biases. Second, when it comes to genetics the climate of Europe is ideal for the preservation and extraction of ancient DNA. Third, there are relatively clear and distinct theoretical models which can be tested by the data, whether to verify or refute.

ResearchBlogging.orgI have already reviewed earlier work in three previous posts, European man perhaps a Middle Eastern farmer, European man perhaps not a Middle Eastern farmer, and Völkerwanderung back with a vengeance. Instead of rehashing everything I’ll take it as a given that you’ve read or skimmed those posts. Rather, let’s move on to a new paper in PLoS Biology, Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities:

In Europe, the Neolithic transition (8,000–4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic.

sommer-nadachowski-2006-figAs I’ve indicated before the archaeological jargon is rather mystifying to me. Some of this is due to translation, the Linear Pottery Culture is abbreviated “LBK” because in the German it is Linearbandkeramik. Rather, I try and focus on some basic concrete parameters: time and space. So we have the first agricultural society with a focus on Central Europe flourishing ~7,000 years before the present. Some now we have the time and space in mind around which we can bracket all the background variables. The big question being asked, and answered, is whether the practitioners of LBK were descendants of Ice Age Europeans who expanded from the “refugia” in the south of Europe during the Last Glacial Maximum (LGM) ~20,000 years ago. To speak intelligently about these issues you need some basic intuition, so you see the map which I found on John Hawks’ weblog showing the line of settlement during the LGM. As the ice retreated presumably the European hunter-gatherers would have rapidly pushed northward, following the species which they consumed.

I’ll pass over the methodological nuts & bolts; you can find them in the paper. Obviously this isn’t technically trivial; extracting, amplifying, and avoiding contamination, from DNA samples on the order of 7,000 years old is awesome. As usual they focused on mtDNA because this is found in much larger quantities than nuclear DNA. They did get a few Y chromosomal results though, though mtDNA is the star of the show here. The mtDNA is the maternal lineage, so it can tell you only so much. Additionally, there may be selection dynamics going on to change the frequencies of some of these variants. But with those caveats in hand I think mtDNA patterns can be very informative because if women are on the move that is a pointer to a classic folk-wandering, where a whole people transplant their culture via migration. Many more British women arrived in the New World than Spanish women, and therein lay one of the crucial factors in the difference between Anglo and Latin America.

The slide show below has all the major figures of interest. I’ve also replicated the full description, and made some minor edits. Please take in the table; much of the paper really presupposes an intuitive familiarity with mtDNA haplogroup frequencies.



mtDNA pairwise Fst by population
Hunter-Gatherers Near East LBK
Near East 4.46 * *
LBK 9.9 3.22 *
Central Europe 3.67 1 4.22

The authors also had an Fst table illustrating genetic distances using mtDNA of ancient and contemporary populations. I’ve cleaned up the table a bit, and standardized the values so that the smallest distance = 1. This is mostly so you can make immediate sense of it. What you clearly see is the enormous genetic distance between Central European hunter-gatherers and LBK, who were present in Germany right before the arrival of farmers. This comes very close to a falsification of the maximalist pots-not-people model, whereby farming spread from its point of origin in Anatolia and the Levant through a process of cultural diffusion, just like the alphabet or the potato. The relatively large distance between ancient and modern populations shouldn’t be too surprising, genetic distances operate across both time and space. There are interesting inferences one can make about the nature of gene flow over the past 10,000 years in Eurasia when viewing the relatively small distance between the two modern populations, but really the important point for the purposes of this paper is the high wall between the two cultures who practice differing modes of production.

In the paper the authors support, tentatively, a classic demic diffusion process. This is basically a very simple model whereby farmers with larger population growth rates expand into the “space” of hunter-gatherers. But as Dienekes Pontikos notes such a process would also be characterized by dilution of the original Middle Eastern “genetic signal” over time. Rather, what we see here seems to be a total transfer for a population across large distances. The authors themselves note that the LBK farmers seem to have followed the interior lines of rivers and flat-bottom plains. Farmers had discovered a new way to exploit nature, but in the end they were still ecologically constrained. The northern two-thirds of Scandinavia still had hunter-gatherer populations down to the period of the classical Greeks. This was not because of the powerful magic wielded by Väinämöinen. The Middle Eastern derived agricultural toolkit no doubt began to run into its natural ecological limits on Europe’s northern fringe. Without knowing anything further I suspect that the death of the southern Sami culture in the face of Norwegian and Swedish expansion in the early modern period was probably driven by the emergence of more systematic agricultural science, which could push the ecological limits beyond the long-standing equilibrium established in the Iron Age.

But I don’t think this is just a story of ecology. It is clearly a story of culture. We assume that culture is easily transferable from society to society. In some ways it is. The original phonetic script of Upper Mesopotamia and Syria seems to have quickly triggered imitation and appropriation from India to Italy within a few centuries of its widespread use by the Aramaeans. But farming is not like the idea of writing. The original farmers seem to have expanded rather slowly initially out of the Middle East. Not only did they perfect the biological character of their crops, they probably perfected the customs and traditions which would go along with farming. A complex suite of explicit rules and implicit norms. Perhaps it was not so easy to simply copy the farming lifestyle? Or, perhaps more interestingly, the hunter-gatherers by and large did not want to copy the farming lifestyle? (this is a tendency among some modern non-farming groups, who would rather work temporarily on farms themselves rather than become full-time obligate peasants) The large genetic distances between the LBK and the hunter-gatherers around them may indicate not only the relatively endogenous growth of the LBK in “virgin” land (e.g., compare to the Yankees of New England in the 17th and 18th century), but, also the emergence of an ideological aversion to mixing with the “savages.” We have plenty of textually attested de-humanization of the “savage” and “barbarian” by the “civilized.” It is likely that the gap between the LBK and the hunter-gatherers of Europe was only somewhat smaller than that between the Aborigines of Australia and Tasmania and the European settlers!

Finally, there’s one last issue I want to highlight: the authors find that many presumably hunter-gatherer lineages are found among the LBK, while very common haplogroups (mtDNA and Y) in Europe today are not found among the LBK or the ancient hunter-gatherers. The clear inference then would be that Europe went through several periods of demographic change and migration within the last 10,000 years. A simple two-way admixture scenario will not suffice. Yesterday I posted this bar plot which contrasted the pattern of ancestry of French vs. French Basque using ADMIXTURE at K = 10:

French

The green element is nearly 100% in Sardinia, and drops off to nearly nothing somewhere around Iran. The light blue component is modal around the Caucasus, though is widely distributed, from Spain to Bengal (yeah, that’s me!) to Sweden. A simple model would be that the light blue arrived with Neolithic agriculturalists, as the Basques are the descendants of the original Ice Age Europeans. But this may not be correct, and our impression of the Basques may be totally false. It is not out of the question now that the Basque culture may have arrived via the ancient leap-frogging of agriculture from fertile regions around the Mediterranean before the seafarers passed into the Atlantic and swept around the western fringe of Iberia. What we may be seeing is a palimpsest of agriculturalists, where the Basques simply lack the last layer.

In any case, one can speculate a lot right. Ancient DNA has allowed us to refute maximalist versions of pots-not-people, but has also overturned our ability to hold to simple robust models. In science you prefer parsimony, unless parsimony simply can’t explain the patterns at hand. I think we’re there at this point.

Citation: Wolfgang Haak, Oleg Balanovsky, Juan J. Sanchez, Sergey Koshel, Valery Zaporozhchenko, Christina J. Adler, Clio S. I. Der Sarkissian, Guido Brandt, Carolin Schwarz, Nicole Nicklisch, Veit Dresely, Barbara Fritsch, Elena Balanovska, Richard Villems, Harald Meller, Kurt W. Alt, Alan Cooper, & Genographic Consortium (2010). Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities PLoS Biology : 10.1371/journal.pbio.1000536

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